Pseudo-shock waves have gained considerable attention in various application fields. This study investigates the effect of bypass flow passage on pseudo-shock waves in dual-mode scramjets. A computational fluid dynamics (CFD)-based approach is employed to examine the influence of bypass flow passages on the pseudo-shock wave. Simulations have been conducted for flow fields within ducts without control measures and those with bypass control implemented. By utilizing bypass flow passages, the structure of pseudo-shock waves in the isolator can be effectively controlled. This method also generates suction flow at the isolator inlet. The findings reveal that the use of bypass flow passages leads to a more stable pseudo-shock wave within the isolator. Furthermore, the bypass flow passage allows for effective control of boundary layer separation at the isolator inlet, demonstrating its critical impact on the stability and behavior of pseudo-shock waves in dual-mode scramjet systems.